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Devising Isolation Forest-Based Method to Investigate the sRNAome of Mycobacterium tuberculosis Using sRNA-seq Data.
Maity, Upasana; Aggarwal, Ritika; Balasubramanian, Rami; Venkatraman, Divya Lakshmi; R Hegde, Shubhada.
Affiliation
  • Maity U; Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India.
  • Aggarwal R; Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India.
  • Balasubramanian R; Novartis Pharmaceuticals, Hyderabad, India.
  • Venkatraman DL; Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India.
  • R Hegde S; Institute of Bioinformatics and Applied Biotechnology, Bengaluru, India.
Bioinform Biol Insights ; 18: 11779322241263674, 2024.
Article de En | MEDLINE | ID: mdl-39091283
ABSTRACT
Small non-coding RNAs (sRNAs) regulate the synthesis of virulence factors and other pathogenic traits, which enables the bacteria to survive and proliferate after host infection. While high-throughput sequencing data have proved useful in identifying sRNAs from the intergenic regions (IGRs) of the genome, it remains a challenge to present a complete genome-wide map of the expression of the sRNAs. Moreover, existing methodologies necessitate multiple dependencies for executing their algorithm and also lack a targeted approach for the de novo sRNA identification. We developed an Isolation Forest algorithm-based method and the tool Prediction Of sRNAs using Isolation Forest for the de novo identification of sRNAs from available bacterial sRNA-seq data (http//posif.ibab.ac.in/). Using this framework, we predicted 1120 sRNAs and 46 small proteins in Mycobacterium tuberculosis. Besides, we highlight the context-dependent expression of novel sRNAs, their probable synthesis, and their potential relevance in stress response mechanisms manifested by M. tuberculosis.
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Texte intégral: 1 Collection: 01-internacional Base de données: MEDLINE Langue: En Journal: Bioinform Biol Insights Année: 2024 Type de document: Article Pays d'affiliation: Inde Pays de publication: États-Unis d'Amérique

Texte intégral: 1 Collection: 01-internacional Base de données: MEDLINE Langue: En Journal: Bioinform Biol Insights Année: 2024 Type de document: Article Pays d'affiliation: Inde Pays de publication: États-Unis d'Amérique